<tool id="ip_points_to_label" name="Convert point coordinates to label map" version="0.3-2"> 
    <description></description>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">galaxy_image_analysis</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="1.15.4">numpy</requirement>
        <requirement type="package" version="0.14.2">scikit-image</requirement>
        <requirement type="package" version="0.23.4">pandas</requirement>
        <requirement type="package" version="0.15.1">tifffile</requirement>
    </requirements> 
    <command detect_errors="aggressive">
    <![CDATA[
        python '$__tool_directory__/points2label.py' '$input' '$output' '$org_file' $has_header
    ]]>
    </command>
    <inputs>
        <param name="input" type="data" format="tabular" label="Point CSV file"/>
        <param name="org_file" type="data" format="tiff" label="Original label image file"/>
        <param name="has_header" type="boolean" checked="false" truevalue="--has_header True" falsevalue="" optional="true" label="Does point file contain header?" /> 
    </inputs>
    <outputs>
        <data name="output" format="tiff"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="points.tsv"/>
            <param name="org_file" value="galaxyIcon_noText.tif"/>
            <output name="output" file="out.tif" ftype="tiff" compare="sim_size"/>
        </test>
    </tests>
    <help>
    **What it does**

    This tool converts points to a label image.
    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 
    </citations>
</tool>